Variant report

Variant	rs10876981
Chromosome Location	chr12:57786897-57786898
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:57785867..57788077-chr12:57824277..57826744,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000179912	Chromatin interaction
ENSG00000258001	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10783823	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10876976	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10876977	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10876978	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10876980	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10876983	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11172165	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11172170	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11172177	0.81[ASN][1000 genomes]
rs11172190	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11172191	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11172205	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11172211	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11172214	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12230111	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12423654	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1284252	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1798710	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2063778	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28504983	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4108243	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4760193	0.82[ASN][1000 genomes]
rs4760228	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4760236	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4760244	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4760305	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4760306	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4760308	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4760348	0.82[EUR][1000 genomes]
rs4760356	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4760357	0.83[ASN][1000 genomes]
rs481196	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs491750	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs492749	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs512223	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs533975	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs537482	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs543410	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs560048	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs568793	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs575153	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6581135	0.83[ASN][1000 genomes]
rs6581136	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6581139	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7132367	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7133366	0.80[EUR][1000 genomes]
rs7303070	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7307059	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7309659	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7313824	0.82[ASN][1000 genomes]
rs7398058	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7980310	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9738004	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046013	chr12:57714676-57895167	Active TSS Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
2	nsv541502	chr12:57714676-57895167	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
3	nsv516655	chr12:57763520-57811414	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57695200-57794600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr12:57704400-57789200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr12:57731400-57789800	Weak transcription	Small Intestine	intestine
4	chr12:57731600-57796000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr12:57736400-57795000	Weak transcription	Right Ventricle	heart
6	chr12:57745000-57787800	Weak transcription	Placenta	Placenta
7	chr12:57753200-57823800	Weak transcription	Esophagus	oesophagus
8	chr12:57761200-57787400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr12:57761400-57789000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr12:57762800-57811800	Weak transcription	Pancreas	Pancrea
11	chr12:57763000-57796800	Weak transcription	Colonic Mucosa	Colon
12	chr12:57763000-57799200	Weak transcription	Psoas Muscle	Psoas
13	chr12:57763000-57800400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr12:57765200-57789200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr12:57765600-57787000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr12:57766000-57787800	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr12:57766200-57795000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr12:57766200-57816000	Weak transcription	Fetal Lung	lung
19	chr12:57768600-57790800	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr12:57770800-57824000	Weak transcription	Gastric	stomach
21	chr12:57774400-57819200	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr12:57777000-57789200	Weak transcription	Brain Hippocampus Middle	brain
23	chr12:57779200-57790000	Strong transcription	Liver	Liver
24	chr12:57779400-57790000	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr12:57779600-57788400	Weak transcription	HepG2	liver
26	chr12:57780200-57788000	Weak transcription	GM12878-XiMat	blood
27	chr12:57780400-57791400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr12:57780400-57795000	Weak transcription	Brain Substantia Nigra	brain
29	chr12:57780600-57788800	Weak transcription	Lung	lung
30	chr12:57780600-57789800	Strong transcription	Primary B cells from peripheral blood	blood
31	chr12:57780600-57795000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr12:57780800-57823200	Weak transcription	Spleen	Spleen
33	chr12:57781200-57795000	Weak transcription	Aorta	Aorta
34	chr12:57781400-57789600	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr12:57782600-57787800	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr12:57783000-57788000	Weak transcription	Ovary	ovary
37	chr12:57783000-57788000	Weak transcription	Thymus	Thymus
38	chr12:57783200-57787600	Weak transcription	Primary T cells from cord blood	blood
39	chr12:57783400-57787200	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr12:57783400-57789000	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr12:57783400-57792800	Weak transcription	K562	blood
42	chr12:57783400-57794600	Weak transcription	Colon Smooth Muscle	Colon
43	chr12:57783600-57797600	Weak transcription	Hela-S3	cervix
44	chr12:57783600-57805000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr12:57783800-57789000	Weak transcription	Brain Germinal Matrix	brain
46	chr12:57783800-57789000	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr12:57783800-57789800	Weak transcription	NH-A	brain
48	chr12:57783800-57799200	Weak transcription	Primary B cells from cord blood	blood
49	chr12:57783800-57800200	Weak transcription	HSMMtube	muscle
50	chr12:57783800-57808600	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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